AMBER Archive (2006)

Subject: RE: AMBER: A dummy atom on the center of solute molecule

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Mon May 29 2006 - 00:51:49 CDT

Dear Ilyas,

I want to do umbrella sampling MD changing the distance between one dummy
atom on the ligand and another molecule to calculate potential of mean
force(PMF).
So, I need to connect that dummy atom with some atoms of the ligand
molecule.

Then I prepared prep file and frcmod file which contains DH(dummy atom). I
can understand that I have to change bond parameter in frcmod file as
following,

-------frcmod file---------
remark goes here
MASS
DU 0.000 0.000 ATTN, need revision

BOND
c2-DU 0.00 0.000 ATTN, need revision

ANGLE
c3-c2-DU 0.000 0.000 ATTN, need revision
c2-DU-c2 0.000 0.000 ATTN, need revision
c2-c2-DU 0.000 0.000 ATTN, need revision
ha-c2-DU 0.000 0.000 ATTN, need revision

By the way, after preparing prep file and frcmod file, I think I need to
manipulate tleap program to yield topology file(parmtop) and coordinate
file(parmcrd) But, DH atom can't be recognize in tleap. So I failed to yield
parmtop and parmcrd. How can I make topology file and coordinate file
which contains dummy atom ?

Thank you
Acci

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Ilyas Yildirim
Sent: Monday, May 29, 2006 1:27 PM
To: Atsutoshi Okabe
Cc: amber_at_scripps.edu
Subject: RE: AMBER: A dummy atom on the center of solute molecule

Dear Acci.

> Firstly, I want to put the dummy atom on the middle point of the double
> bond(C=C). But,I couldn't put the dummy atom on the correct middle point
of
> the double bond because xleap graphics is three dimensions using
> mouse(i.e.I can put the atom correctly on x-y plane, but I can't put
> correctly along z-axis ) How can I put
> the dummy atom on correct middle point of the double bond ?

The question is NOT to put the dummy atom in an EXACT location. What do u
need to do with this dummy atom? If u dont connect that dummy atom to some
atoms, in the MD simulation, it is going to fly away from that position.
So, if u connect that dummy atom with some atoms, and define the bond
lengths of those bonds in the .frcmod file, in the minimization process,
it's going to come to the right position.

> Secondly, I executed antechamber program to make prep file of ligand
> molecule as following,
>
> antechamber -i BUT.pdb -fi pdb -o BUT.prep -fo prepi
>
> And, I send you BUT.pdb file and BUT.prep file
>
> I doubt the following line form in prep file ,
>
> 16 X 1 0 1 3.247 180.000 nan 0.00000
>
> Do you think this line is right ?

No, this is not right. It should have the dummy atom name in it (but I
dont see it).

PS: Send your emails to the AMBER mailing list. Someone else might help u,
too. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------
  • application/octet-stream attachment: BUT.prep

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